We’ve observed this behaviour when using links in bullet lists, under some conditions. Here is the thread for that.
If you aren’t using lists, perhaps the problem is more widespread? I had difficulty reproducing that one at first because it required a very precise sequence of events to trigger, so if you have another case, I may need a similar level of specificity. I don’t for example get any kind of link spreading by just typing, pasting a raw URL and then typing some more and pressing return into a fresh new binder item with nothing else in it.
I would note that disabling Automatically detect web addresses, in the Corrections options tab, would dodge the problem entirely. Whether making links by hand is more or less work than removing unintentional links after the fact is probably negligible though; depends on how often you see this happen vs how many links you add that you want to be clickable.
So, congratulations by the way that you managed to create a program that is not only perfect for its original purpose but also fantastic for a lot of other things that have to do with writing.
That’s easily explained by it being somewhat of a myth that Scrivener was made just for novelists. It was always meant to be a general purpose writing tool. 
Thanks for the kind words!